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Topics:
Rendering & Ray Tracing
Type:
Talk
Event:
SIGGRAPH
Year:
2019
Session ID:
SIG919
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Abstract:
This talk will present techniques and performance results for high-fidelity rendering of state-of-the-art biomolecular and cellular simulations using NVIDIA RTX ray tracing hardware with OptiX and Vulkan APIs. We'll introduce the latest technical advances in the OptiX ray tracing engines in VMD, which are used for interactive ray tracing and in-situ and post-hoc visualization of petascale molecular dynamics simulations. We'll describe how to quickly and easily adapted the mature OptiX ray tracing engine in VMD to support RTX hardware acceleration using key language features of CUDA and C++ while maintaining full performance. We'll also share RTX ray tracing performance results for a range of visualization scenarios, including omnidirectional panoramic rendering for VR. In addition, we'll discuss ongoing work on interactive ray tracing of molecular dynamics trajectories (time series data) and easy deployment using NGC containers and Amazon EC2 AMIs.
This talk will present techniques and performance results for high-fidelity rendering of state-of-the-art biomolecular and cellular simulations using NVIDIA RTX ray tracing hardware with OptiX and Vulkan APIs. We'll introduce the latest technical advances in the OptiX ray tracing engines in VMD, which are used for interactive ray tracing and in-situ and post-hoc visualization of petascale molecular dynamics simulations. We'll describe how to quickly and easily adapted the mature OptiX ray tracing engine in VMD to support RTX hardware acceleration using key language features of CUDA and C++ while maintaining full performance. We'll also share RTX ray tracing performance results for a range of visualization scenarios, including omnidirectional panoramic rendering for VR. In addition, we'll discuss ongoing work on interactive ray tracing of molecular dynamics trajectories (time series data) and easy deployment using NGC containers and Amazon EC2 AMIs.  Back
 
Topics:
Rendering & Ray Tracing, In-Situ & Scientific Visualization
Type:
Talk
Event:
GTC Silicon Valley
Year:
2019
Session ID:
S9589
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Abstract:
We'll showcase the latest successes with GPU acceleration of challenging molecular simulation analysis tasks on the latest Volta and Turing GPUs paired with both Intel and IBM/OpenPOWER CPUs on petascale computers such as ORNL Summit. This presentation will highlight the performance benefits obtained from die-stacked memory, NVLink interconnects, and the use of advanced features of CUDA such as just-in-time compilation to increase the performance of key analysis algorithms. We will present results obtained with OpenACC parallel programming directives, as well as discuss current challenges and future opportunities. We'll also describe GPU-Accelerated machine learning algorithms for tasks such as clustering of structures resulting from molecular dynamics simulations. To make our tools easy to deploy for non-tradtional users of HPC, we publish GPU-Accelerated container images in NGC, and Amazon EC2 AMIs for GPU instance types.
We'll showcase the latest successes with GPU acceleration of challenging molecular simulation analysis tasks on the latest Volta and Turing GPUs paired with both Intel and IBM/OpenPOWER CPUs on petascale computers such as ORNL Summit. This presentation will highlight the performance benefits obtained from die-stacked memory, NVLink interconnects, and the use of advanced features of CUDA such as just-in-time compilation to increase the performance of key analysis algorithms. We will present results obtained with OpenACC parallel programming directives, as well as discuss current challenges and future opportunities. We'll also describe GPU-Accelerated machine learning algorithms for tasks such as clustering of structures resulting from molecular dynamics simulations. To make our tools easy to deploy for non-tradtional users of HPC, we publish GPU-Accelerated container images in NGC, and Amazon EC2 AMIs for GPU instance types.  Back
 
Topics:
HPC and Supercomputing, In-Situ & Scientific Visualization
Type:
Talk
Event:
GTC Silicon Valley
Year:
2019
Session ID:
S9594
Streaming:
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Abstract:

NAMD and VMD provide state-of-the-art molecular simulation, analysis, and visualization tools that leverage a panoply of GPU acceleration technologies to achieve performance levels that enable scientists to routinely apply research methods that were formerly too computationally demanding to be practical. To make state-of-the-art MD simulation and computational microscopy workflows available to a broader range of molecular scientists including non-traditional users of HPC systems, our center has begun producing pre-configured container images and Amazon EC2 AMIs that streamline deployment, particularly for specialized occasional-use workflows, e.g., for refinement of atomic structures obtained through cryo-electron microscopy. This talk will describe the latest technological advances in NAMD and VMD, using CUDA, OpenACC, and OptiX, including early results on ORNL Summit, state-of-the-art RTX hardware ray tracing on Turing GPUs, and easy deployment using containers and cloud computing infrastructure.

NAMD and VMD provide state-of-the-art molecular simulation, analysis, and visualization tools that leverage a panoply of GPU acceleration technologies to achieve performance levels that enable scientists to routinely apply research methods that were formerly too computationally demanding to be practical. To make state-of-the-art MD simulation and computational microscopy workflows available to a broader range of molecular scientists including non-traditional users of HPC systems, our center has begun producing pre-configured container images and Amazon EC2 AMIs that streamline deployment, particularly for specialized occasional-use workflows, e.g., for refinement of atomic structures obtained through cryo-electron microscopy. This talk will describe the latest technological advances in NAMD and VMD, using CUDA, OpenACC, and OptiX, including early results on ORNL Summit, state-of-the-art RTX hardware ray tracing on Turing GPUs, and easy deployment using containers and cloud computing infrastructure.

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Topics:
Application Design & Porting Techniques
Type:
Talk
Event:
Supercomputing
Year:
2018
Session ID:
SC1803
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Abstract:
Advances in OptiX and RTX ray tracing bring tremendous performance improvements for rendering scenes from technical and scientific visualization workloads. New OptiX acceleration structures enable rendering of scenes with much greater geometric complexity on a single GPU, making it possible for scientists to interactively render high fidelity visualizations of complex scenes. This talk will describe the results from the adaptation of VMD, a widely used molecular visualization tool with over 100,000 users,to exploit the latest capabilities of OptiX.
Advances in OptiX and RTX ray tracing bring tremendous performance improvements for rendering scenes from technical and scientific visualization workloads. New OptiX acceleration structures enable rendering of scenes with much greater geometric complexity on a single GPU, making it possible for scientists to interactively render high fidelity visualizations of complex scenes. This talk will describe the results from the adaptation of VMD, a widely used molecular visualization tool with over 100,000 users,to exploit the latest capabilities of OptiX.   Back
 
Topics:
Rendering & Ray Tracing
Type:
Talk
Event:
SIGGRAPH
Year:
2018
Session ID:
SIG1849
Streaming:
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Abstract:
State-of-the-art experimental imaging and molecular dynamics simulations pose many challenges for effective visualization and analysis due to the growing size, timescale, and complexity of the structures under study. This talk will describe how a variety of new and emerging visualization technologies can be used to address these challenges. This talk will describe our approach to adapt VMD, a widely used molecular visualization and analysis tool, to exploit new rasterization APIs such as EGL and Vulkan, and the NVIDIA OptiX ray tracing API for both interactive and in-situ or post-hoc molecular visualization on workstations, clouds, and supercomputers. Commodity head mounted VR displays (HMDs) offer a tremendous opportunity to make immersive molecular visualization techniques broadly available to molecular scientists, but they present many performance challenges for both rasterization- and ray tracing-based visualization. We present results from our ongoing work adapting VMD to support popular VR HMDs.
State-of-the-art experimental imaging and molecular dynamics simulations pose many challenges for effective visualization and analysis due to the growing size, timescale, and complexity of the structures under study. This talk will describe how a variety of new and emerging visualization technologies can be used to address these challenges. This talk will describe our approach to adapt VMD, a widely used molecular visualization and analysis tool, to exploit new rasterization APIs such as EGL and Vulkan, and the NVIDIA OptiX ray tracing API for both interactive and in-situ or post-hoc molecular visualization on workstations, clouds, and supercomputers. Commodity head mounted VR displays (HMDs) offer a tremendous opportunity to make immersive molecular visualization techniques broadly available to molecular scientists, but they present many performance challenges for both rasterization- and ray tracing-based visualization. We present results from our ongoing work adapting VMD to support popular VR HMDs.  Back
 
Topics:
In-Situ & Scientific Visualization, Rendering & Ray Tracing
Type:
Talk
Event:
GTC Silicon Valley
Year:
2018
Session ID:
S8665
Streaming:
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Abstract:
Are you readying your application for dense multi-GPU compute hardware like the NVIDIA DGX or ORNL Summit? Are you sure your CPUs and GPUs are all working to their capabilities? Are you looking for a tool to squeeze out that last bit of performance? Come and learn how the new NVIDIA Nsight Systems can help you maximize the performance of your simulation and visualization applications on GPU-accelerated clusters. Learn suggested techniques and best practices for optimizing HPC workloads. NVIDIA engineers and the developers of molecular modeling tools at University of Illinois will share their experiences using the NVIDIA Nsight Systems to analyze and optimize several of their HPC applications, including NAMD, VMD, and Lattice Microbes. The session will highlight several intermediate and advanced profiling techniques and will demonstrate how incorporation of NVTX profiling hooks into the application can help focus profiling activity and improve clarity of profiling results in complex HPC apps.
Are you readying your application for dense multi-GPU compute hardware like the NVIDIA DGX or ORNL Summit? Are you sure your CPUs and GPUs are all working to their capabilities? Are you looking for a tool to squeeze out that last bit of performance? Come and learn how the new NVIDIA Nsight Systems can help you maximize the performance of your simulation and visualization applications on GPU-accelerated clusters. Learn suggested techniques and best practices for optimizing HPC workloads. NVIDIA engineers and the developers of molecular modeling tools at University of Illinois will share their experiences using the NVIDIA Nsight Systems to analyze and optimize several of their HPC applications, including NAMD, VMD, and Lattice Microbes. The session will highlight several intermediate and advanced profiling techniques and will demonstrate how incorporation of NVTX profiling hooks into the application can help focus profiling activity and improve clarity of profiling results in complex HPC apps.  Back
 
Topics:
Performance Optimization, Tools & Libraries, HPC and Supercomputing
Type:
Talk
Event:
GTC Silicon Valley
Year:
2018
Session ID:
S8718
Streaming:
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Abstract:
In 2007, NAMD was the first full-featured production molecular dynamics software to use CUDA for accelerating its costliest computations. We'll describe our latest efforts, techniques, and results in our quest to optimize NAMD to make best use of the tremendous computational capabilities of state-of-the-art Volta GPUs, particularly in new dense node configurations such as the NVIDIA DGX and ORNL Summit systems that feature NVLink-connected GPUs. In existence now for over 20 years, NAMD is a sophisticated parallel molecular dynamics program. NAMD development has emphasized parallel scalability to support large-size and long-timescale biomolecular simulations running on petascale supercomputers. As GPU technology has evolved, NAMD has benefited from moving greater amounts of work to the GPU. NVIDIA's release of Volta has now shifted the balance almost entirely to the GPU, with the small remaining CPU calculations often posing bottlenecks to NAMD's performance. Attendees will learn optimization strategies and pitfalls for achieving higher performance as Amdahl's Law poses an ever increasing challenge for mature GPU-accelerated codes like NAMD.
In 2007, NAMD was the first full-featured production molecular dynamics software to use CUDA for accelerating its costliest computations. We'll describe our latest efforts, techniques, and results in our quest to optimize NAMD to make best use of the tremendous computational capabilities of state-of-the-art Volta GPUs, particularly in new dense node configurations such as the NVIDIA DGX and ORNL Summit systems that feature NVLink-connected GPUs. In existence now for over 20 years, NAMD is a sophisticated parallel molecular dynamics program. NAMD development has emphasized parallel scalability to support large-size and long-timescale biomolecular simulations running on petascale supercomputers. As GPU technology has evolved, NAMD has benefited from moving greater amounts of work to the GPU. NVIDIA's release of Volta has now shifted the balance almost entirely to the GPU, with the small remaining CPU calculations often posing bottlenecks to NAMD's performance. Attendees will learn optimization strategies and pitfalls for achieving higher performance as Amdahl's Law poses an ever increasing challenge for mature GPU-accelerated codes like NAMD.  Back
 
Topics:
Computational Biology & Chemistry, HPC and Supercomputing
Type:
Talk
Event:
GTC Silicon Valley
Year:
2018
Session ID:
S8727
Streaming:
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Abstract:
We'll showcase recent successes in the use of GPUs to accelerate challenging molecular simulation analysis tasks on the latest Volta-based Tesla V100 GPUs on both Intel and IBM/OpenPOWER hardware platforms, and with large scale runs on petascale computers such as ORNL Summit. We'll highlight the performance benefits obtained from die-stacked memory on Tesla V100, the NVLink interconnect on the IBM OpenPOWER platforms, and the use of advanced features of CUDA, Volta's new Tensor units, and just-in-time compilation to increase the performance of key analysis algorithms. We'll present results obtained with OpenACC parallel programming directives, current challenges, and future opportunities. Finally, we'll describe GPU-accelerated machine learning algorithms for tasks such as clustering of structures resulting from molecular dynamics simulations.
We'll showcase recent successes in the use of GPUs to accelerate challenging molecular simulation analysis tasks on the latest Volta-based Tesla V100 GPUs on both Intel and IBM/OpenPOWER hardware platforms, and with large scale runs on petascale computers such as ORNL Summit. We'll highlight the performance benefits obtained from die-stacked memory on Tesla V100, the NVLink interconnect on the IBM OpenPOWER platforms, and the use of advanced features of CUDA, Volta's new Tensor units, and just-in-time compilation to increase the performance of key analysis algorithms. We'll present results obtained with OpenACC parallel programming directives, current challenges, and future opportunities. Finally, we'll describe GPU-accelerated machine learning algorithms for tasks such as clustering of structures resulting from molecular dynamics simulations.  Back
 
Topics:
Computational Biology & Chemistry, HPC and Supercomputing
Type:
Talk
Event:
GTC Silicon Valley
Year:
2018
Session ID:
S8709
Streaming:
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Abstract:
State-of-the-art molecular simulations pose many challenges for effective visualization and analysis due to their size, timescale, and the growing complexity of the structures under study. Fortunately, a panoply of new and emerging technologies can address these challenges. We'll describe our experiences and progress adapting VMD, a widely used molecular visualization and analysis tool, to exploit new rasterization APIs such as EGL and Vulkan, and the NVIDIA OptiX ray tracing API for interactive, in-situ, and post-hoc molecular visualization on workstations, clouds, and supercomputers, highlighting the latest results on IBM POWER hardware. Commodity VR headsets offer a tremendous opportunity to make immersive molecular visualization broadly available to molecular scientists, but they present many performance challenges for both rasterization- and ray tracing-based visualization. We'll present results from our ongoing work adapting VMD to support popular VR HMDs.
State-of-the-art molecular simulations pose many challenges for effective visualization and analysis due to their size, timescale, and the growing complexity of the structures under study. Fortunately, a panoply of new and emerging technologies can address these challenges. We'll describe our experiences and progress adapting VMD, a widely used molecular visualization and analysis tool, to exploit new rasterization APIs such as EGL and Vulkan, and the NVIDIA OptiX ray tracing API for interactive, in-situ, and post-hoc molecular visualization on workstations, clouds, and supercomputers, highlighting the latest results on IBM POWER hardware. Commodity VR headsets offer a tremendous opportunity to make immersive molecular visualization broadly available to molecular scientists, but they present many performance challenges for both rasterization- and ray tracing-based visualization. We'll present results from our ongoing work adapting VMD to support popular VR HMDs.  Back
 
Topics:
In-Situ & Scientific Visualization, Virtual Reality & Augmented Reality, HPC and Supercomputing
Type:
Talk
Event:
GTC Silicon Valley
Year:
2017
Session ID:
S7391
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Abstract:
We'll present the latest advances in the use of NVIDIA Optix for high-fidelity rendering of state-of-the-art biomolecular and cellular simulations. We'll present the latest technical advances in the OptiX-based ray -racing engines in VMD, which are heavily used for both interactive progressive ray-tracing (local and remote), and for batch mode in-situ or post-hoc visualization of petascale molecular dynamics simulations.
We'll present the latest advances in the use of NVIDIA Optix for high-fidelity rendering of state-of-the-art biomolecular and cellular simulations. We'll present the latest technical advances in the OptiX-based ray -racing engines in VMD, which are heavily used for both interactive progressive ray-tracing (local and remote), and for batch mode in-situ or post-hoc visualization of petascale molecular dynamics simulations.  Back
 
Topics:
Rendering & Ray Tracing, In-Situ & Scientific Visualization, Healthcare and Life Sciences, HPC and Supercomputing
Type:
Talk
Event:
GTC Silicon Valley
Year:
2017
Session ID:
S7452
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Abstract:

We'll showcase recent successes in the use of GPUs to accelerate challenging molecular simulation analysis tasks on the latest NVIDIA?Tesla?P100 GPUs on both Intel and IBM/OpenPOWER hardware platforms, and large-scale runs on petascale computers such as Titan and Blue Waters. We'll highlight the performance benefits obtained from die-stacked memory on the Tesla P100, the NVIDIA NVLink# interconnect on the IBM "Minsky" platform, and the use of NVIDIA CUDA?just-in-time compilation to increase the performance of data-driven algorithms. We will present results obtained with OpenACC parallel programming directives, current challenges, and future opportunities. Finally, we'll describe GPU-accelerated machine learning algorithms for tasks such as clustering of structures resulting from molecular dynamics simulations.

We'll showcase recent successes in the use of GPUs to accelerate challenging molecular simulation analysis tasks on the latest NVIDIA?Tesla?P100 GPUs on both Intel and IBM/OpenPOWER hardware platforms, and large-scale runs on petascale computers such as Titan and Blue Waters. We'll highlight the performance benefits obtained from die-stacked memory on the Tesla P100, the NVIDIA NVLink# interconnect on the IBM "Minsky" platform, and the use of NVIDIA CUDA?just-in-time compilation to increase the performance of data-driven algorithms. We will present results obtained with OpenACC parallel programming directives, current challenges, and future opportunities. Finally, we'll describe GPU-accelerated machine learning algorithms for tasks such as clustering of structures resulting from molecular dynamics simulations.

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Topics:
HPC and Supercomputing, Accelerated Data Science, Computational Biology & Chemistry
Type:
Talk
Event:
GTC Silicon Valley
Year:
2017
Session ID:
S7382
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Abstract:

The tremendous successes that GPUs have had in accelerating molecular simulations must continue to be matched by advances in their application to challenging simulation preparation, analysis, and visualization tasks. We will describe how the latest developments in the molecular visualization tool VMD exploit GPUs using exciting new features of CUDA, OpenACC, EGL, and OptiX to accelerate key science tasks on clouds, clusters, and petascale computers. We will summarize our early experiences and performance results on GPU-accelerated OpenPOWER platforms with an eye toward the challenges and opportunities posed by the upcoming DOE Summit and Sierra systems.

The tremendous successes that GPUs have had in accelerating molecular simulations must continue to be matched by advances in their application to challenging simulation preparation, analysis, and visualization tasks. We will describe how the latest developments in the molecular visualization tool VMD exploit GPUs using exciting new features of CUDA, OpenACC, EGL, and OptiX to accelerate key science tasks on clouds, clusters, and petascale computers. We will summarize our early experiences and performance results on GPU-accelerated OpenPOWER platforms with an eye toward the challenges and opportunities posed by the upcoming DOE Summit and Sierra systems.

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Topics:
HPC and Supercomputing
Type:
Talk
Event:
Supercomputing
Year:
2016
Session ID:
SC6127
Streaming:
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Abstract:

We'll showcase recent successes in the use of GPUs to accelerate challenging molecular visualization and analysis tasks on hardware platforms ranging from commodity desktop computers to the latest GPU-accelerated petascale supercomputers by Cray and IBM. We'll highlight the use of in-situ ray tracing and rasterization combined with GPU-accelerated video streaming for high-interactivity remote visualization, CUDA just-in-time compilation to increase the performance of data-driven visualization and analysis algorithms, and we'll describe new, GPU-accelerated, MD trajectory clustering algorithms.

We'll showcase recent successes in the use of GPUs to accelerate challenging molecular visualization and analysis tasks on hardware platforms ranging from commodity desktop computers to the latest GPU-accelerated petascale supercomputers by Cray and IBM. We'll highlight the use of in-situ ray tracing and rasterization combined with GPU-accelerated video streaming for high-interactivity remote visualization, CUDA just-in-time compilation to increase the performance of data-driven visualization and analysis algorithms, and we'll describe new, GPU-accelerated, MD trajectory clustering algorithms.

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Topics:
In-Situ & Scientific Visualization, Computational Biology & Chemistry, Rendering & Ray Tracing
Type:
Talk
Event:
GTC Silicon Valley
Year:
2016
Session ID:
S6253
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Abstract:
We'll describe the adaptation of the popular molecular graphics program VMD for interactive ray tracing using NVIDIA OptiX, on computers ranging from laptops all the way up to large NVIDIA VCA GPU clusters, and petascale supercomputers such as the Blue Waters and Titan. We'll highlight the new OptiX 3.8 progressive rendering and remote device APIs, and show how they are using VMD for both local and remote VCA rendering. We'll highlight the use of OptiX GPU ray tracing for interactive panoramic and omnidirectional projections suited to planetariums, fulldome theaters, and VR headsets (HMDs) such as the Oculus Rift. The session will present the latest VMD+OptiX ray tracing performance data for workstation, VCA GPU clusters, and supercomputers.
We'll describe the adaptation of the popular molecular graphics program VMD for interactive ray tracing using NVIDIA OptiX, on computers ranging from laptops all the way up to large NVIDIA VCA GPU clusters, and petascale supercomputers such as the Blue Waters and Titan. We'll highlight the new OptiX 3.8 progressive rendering and remote device APIs, and show how they are using VMD for both local and remote VCA rendering. We'll highlight the use of OptiX GPU ray tracing for interactive panoramic and omnidirectional projections suited to planetariums, fulldome theaters, and VR headsets (HMDs) such as the Oculus Rift. The session will present the latest VMD+OptiX ray tracing performance data for workstation, VCA GPU clusters, and supercomputers.  Back
 
Topics:
Rendering & Ray Tracing, In-Situ & Scientific Visualization
Type:
Talk
Event:
GTC Silicon Valley
Year:
2016
Session ID:
S6258
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Abstract:
Commodity head-mounted displays (HMDs) offer a tremendous opportunity to make immersive molecular visualization techniques broadly available. HMDs offer the promise of intuitive exploration of large molecular complexes and their dynamics, but their requirement for low-latency, high-frame-rate display presents a formidable challenge for high-quality remote ray tracing at distant HPC centers. We'll present a new, interactive ray-tracing system for remote visualization with HMDs, implemented within the popular molecular visualization tool VMD using a combination of interactive OptiX ray tracing, omnidirectional stereoscopic projection, H.264 video streaming, and high performance OpenGL rasterization.
Commodity head-mounted displays (HMDs) offer a tremendous opportunity to make immersive molecular visualization techniques broadly available. HMDs offer the promise of intuitive exploration of large molecular complexes and their dynamics, but their requirement for low-latency, high-frame-rate display presents a formidable challenge for high-quality remote ray tracing at distant HPC centers. We'll present a new, interactive ray-tracing system for remote visualization with HMDs, implemented within the popular molecular visualization tool VMD using a combination of interactive OptiX ray tracing, omnidirectional stereoscopic projection, H.264 video streaming, and high performance OpenGL rasterization.  Back
 
Topics:
Virtual Reality & Augmented Reality, In-Situ & Scientific Visualization, Rendering & Ray Tracing
Type:
Talk
Event:
GTC Silicon Valley
Year:
2016
Session ID:
S6261
Streaming:
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Abstract:
This talk will showcase recent successes in the use of GPUs to accelerate challenging molecular visualization and analysis tasks on hardware platforms ranging from commodity desktop computers to the latest Cray supercomputers. This presentation will highlight the use of in-place OpenGL rendering and GPU ray tracing for interactive and batch mode rendering of images and movies, CUDA just-in-time (JIT) compilation for increasing the performance of data-driven visualization and analysis algorithms, and GPU accelerated analysis of results of hybrid structure determination methods that combine data from cryo-electron microscopy and X-ray crystallography with all-atom molecular dynamics simulations.
This talk will showcase recent successes in the use of GPUs to accelerate challenging molecular visualization and analysis tasks on hardware platforms ranging from commodity desktop computers to the latest Cray supercomputers. This presentation will highlight the use of in-place OpenGL rendering and GPU ray tracing for interactive and batch mode rendering of images and movies, CUDA just-in-time (JIT) compilation for increasing the performance of data-driven visualization and analysis algorithms, and GPU accelerated analysis of results of hybrid structure determination methods that combine data from cryo-electron microscopy and X-ray crystallography with all-atom molecular dynamics simulations.  Back
 
Topics:
Visualization - In-Situ & Scientific, Big Data Analytics, Life & Material Science
Type:
Talk
Event:
GTC Silicon Valley
Year:
2015
Session ID:
S5371
Streaming:
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Abstract:
This session will describe the adaptation of the popular molecular graphics program VMD to support both batch and interactive ray tracing using NVIDIA OptiX, on computers ranging from laptops all the way up to large scale Cray XK7 supercomputers such as Blue Waters and Titan. We will describe the benefits of custom VMD-specific geometric primitives and memory layouts, and relate our experiences adapting the Tachyon CPU-based ray tracing engine used by VMD, to NVIDIA's OptiX GPU ray tracing framework. The session will present performance data for workstation and supercomputer class visualizations, integration of OptiX into VMD, interactive ray tracing, many example movies and visualizations, and avenues for further improvement.
This session will describe the adaptation of the popular molecular graphics program VMD to support both batch and interactive ray tracing using NVIDIA OptiX, on computers ranging from laptops all the way up to large scale Cray XK7 supercomputers such as Blue Waters and Titan. We will describe the benefits of custom VMD-specific geometric primitives and memory layouts, and relate our experiences adapting the Tachyon CPU-based ray tracing engine used by VMD, to NVIDIA's OptiX GPU ray tracing framework. The session will present performance data for workstation and supercomputer class visualizations, integration of OptiX into VMD, interactive ray tracing, many example movies and visualizations, and avenues for further improvement.  Back
 
Topics:
Rendering & Ray Tracing, Visualization - In-Situ & Scientific, Media and Entertainment
Type:
Talk
Event:
GTC Silicon Valley
Year:
2015
Session ID:
S5386
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Abstract:
We describe the adaptation of VMD, a popular molecular visualization and analysis tool, to exploit the Tesla K20X GPU for acceleration of large scale molecular visualization runs on Cray XK7 petascale supercomputers such as Blue Waters and Titan. We will describe ray tracing performance benefits and memory efficiency optimizations achieved through the use of custom geometric primitives and triangle mesh formats, and relate our experiences adapting the Tachyon CPU-based ray tracing engine used by VMD, to NVIDIA's OptiX GPU ray tracing framework. We will present performance data for large visualization runs on the Cray XK7, discuss our approach to integrating OptiX into VMD, and describe avenues for further improvement.
We describe the adaptation of VMD, a popular molecular visualization and analysis tool, to exploit the Tesla K20X GPU for acceleration of large scale molecular visualization runs on Cray XK7 petascale supercomputers such as Blue Waters and Titan. We will describe ray tracing performance benefits and memory efficiency optimizations achieved through the use of custom geometric primitives and triangle mesh formats, and relate our experiences adapting the Tachyon CPU-based ray tracing engine used by VMD, to NVIDIA's OptiX GPU ray tracing framework. We will present performance data for large visualization runs on the Cray XK7, discuss our approach to integrating OptiX into VMD, and describe avenues for further improvement.  Back
 
Topics:
Rendering & Ray Tracing, Molecular Dynamics, Scientific Visualization, HPC and Supercomputing
Type:
Talk
Event:
GTC Silicon Valley
Year:
2014
Session ID:
S4400
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Abstract:
We present recent successes in the use of GPUs to accelerate challenging molecular visualization and analysis tasks on hardware platforms ranging from commodity desktop computers to the latest Cray XK7 supercomputers. This talk will focus on recent algorithm developments and the applicability and efficient use of new CUDA features on state-of-the-art Kepler GPUs. We will present the latest performance results for GPU accelerated trajectory analysis runs on Cray XK7 petascale systems and GPU-accelerated workstation platforms. We will conclude with a discussion of ongoing work and future opportunities for GPU acceleration, particularly as applied to the analysis of petascale simulations of large biomolecular complexes and long simulation timescales.
We present recent successes in the use of GPUs to accelerate challenging molecular visualization and analysis tasks on hardware platforms ranging from commodity desktop computers to the latest Cray XK7 supercomputers. This talk will focus on recent algorithm developments and the applicability and efficient use of new CUDA features on state-of-the-art Kepler GPUs. We will present the latest performance results for GPU accelerated trajectory analysis runs on Cray XK7 petascale systems and GPU-accelerated workstation platforms. We will conclude with a discussion of ongoing work and future opportunities for GPU acceleration, particularly as applied to the analysis of petascale simulations of large biomolecular complexes and long simulation timescales.  Back
 
Topics:
Molecular Dynamics, Big Data Analytics, Scientific Visualization, HPC and Supercomputing
Type:
Talk
Event:
GTC Silicon Valley
Year:
2014
Session ID:
S4410
Streaming:
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Abstract:

VMD is a tool for preparing, analyzing, and visualizing molecular dynamics simulations, with particular emphasis on large biomolecular systems, including drug targets such as the bacterial ribosome, and large viruses such as HIV.The computational challenges posed by large simulations present a significant hurdle for simulation and analysis tools. GPUs provide unprecedented computational capabilities at a very low cost, making it possible for applications like VMD to accelerate tasks that would otherwise be beyond our grasp. The ubiquitous nature of powerful GPUs on hardware ranging from tablets to supercomputers has allowed us to make a significant investment in developing GPU algorithms for a broad range of uses covering everything from ion placement during simulation preparation to photorealistic ray tracing of movies on hundreds of supercomputer nodes.Join us for this webinar as John Stone, Senior Research Programmer, University of Illinois provides an overview of the GPU-accelerated features of VMD and how they can be used to speed up a wide range of simulation preparation, analysis, and visualization tasks today, along with a roadmap of things to come in the future. 

VMD is a tool for preparing, analyzing, and visualizing molecular dynamics simulations, with particular emphasis on large biomolecular systems, including drug targets such as the bacterial ribosome, and large viruses such as HIV.The computational challenges posed by large simulations present a significant hurdle for simulation and analysis tools. GPUs provide unprecedented computational capabilities at a very low cost, making it possible for applications like VMD to accelerate tasks that would otherwise be beyond our grasp. The ubiquitous nature of powerful GPUs on hardware ranging from tablets to supercomputers has allowed us to make a significant investment in developing GPU algorithms for a broad range of uses covering everything from ion placement during simulation preparation to photorealistic ray tracing of movies on hundreds of supercomputer nodes.Join us for this webinar as John Stone, Senior Research Programmer, University of Illinois provides an overview of the GPU-accelerated features of VMD and how they can be used to speed up a wide range of simulation preparation, analysis, and visualization tasks today, along with a roadmap of things to come in the future. 

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Topics:
Molecular Dynamics
Type:
Webinar
Event:
GTC Webinars
Year:
2014
Session ID:
GTCE075
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Abstract:

Molecular dynamics simulations provide a powerful tool for probing the dynamics of cellular processes at atomic and nanosecond resolution not achievable by experimental methods alone. We describe how GPU-accelerated petascale supercomputers are enabling studies of large biomolecular systems such as the HIV virus in all-atom detail for the first time.

Molecular dynamics simulations provide a powerful tool for probing the dynamics of cellular processes at atomic and nanosecond resolution not achievable by experimental methods alone. We describe how GPU-accelerated petascale supercomputers are enabling studies of large biomolecular systems such as the HIV virus in all-atom detail for the first time.

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Topics:
HPC and Supercomputing
Type:
Talk
Event:
Supercomputing
Year:
2013
Session ID:
SC3111
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Abstract:

This talk will present recent successes in the use of GPUs to accelerate interactive molecular visualization and analysis tasks on hardware platforms ranging from commodity desktop computers to the latest Cray XK7 supercomputers. The talk will focus on recent algorithm algorithm developments and the applicability and efficient use of new CUDA features on state-of-the-art Kepler GPUs. Will present the latest performance results for GPU accelerated trajectory analysis runs on the Blue Waters Cray XK7 and other GPU-accelerated HPC platforms, and conclude with a discussion of ongoing work and future opportunities for GPU acceleration, particularly as applied to the analysis of petascale simulations of large biomolecular complexes and long simulation timescales.

This talk will present recent successes in the use of GPUs to accelerate interactive molecular visualization and analysis tasks on hardware platforms ranging from commodity desktop computers to the latest Cray XK7 supercomputers. The talk will focus on recent algorithm algorithm developments and the applicability and efficient use of new CUDA features on state-of-the-art Kepler GPUs. Will present the latest performance results for GPU accelerated trajectory analysis runs on the Blue Waters Cray XK7 and other GPU-accelerated HPC platforms, and conclude with a discussion of ongoing work and future opportunities for GPU acceleration, particularly as applied to the analysis of petascale simulations of large biomolecular complexes and long simulation timescales.

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Topics:
Quantum Chemistry, Large Scale Data Visualization & In-Situ Graphics
Type:
Talk
Event:
GTC Silicon Valley
Year:
2013
Session ID:
S3097
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Abstract:

This talk will present recent successes in the use of GPUs to accelerate interactive molecular visualization and analysis tasks on desktop computers, and batch-mode simulation and analysis jobs on GPU-accelerated HPC clusters. We'll present Fermi-specific algorithms and optimizations and compare with those for other devices. We'll also present performance and performance/watt results for VMD analysis calculations on GPU clusters, and conclude with a discussion of ongoing work and future opportunities for GPU acceleration, particularly as applied to the analysis of petascale simulations of large biomolecular complexes and long simulation timescales.

This talk will present recent successes in the use of GPUs to accelerate interactive molecular visualization and analysis tasks on desktop computers, and batch-mode simulation and analysis jobs on GPU-accelerated HPC clusters. We'll present Fermi-specific algorithms and optimizations and compare with those for other devices. We'll also present performance and performance/watt results for VMD analysis calculations on GPU clusters, and conclude with a discussion of ongoing work and future opportunities for GPU acceleration, particularly as applied to the analysis of petascale simulations of large biomolecular complexes and long simulation timescales.

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Topics:
Molecular Dynamics
Type:
Talk
Event:
GTC Silicon Valley
Year:
2012
Session ID:
S2142
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Speakers:
John Stone
- University of Illinois at Urbana-Champaign
 
Topics:
Molecular Dynamics, Life & Material Science
Type:
Talk
Event:
Supercomputing
Year:
2010
Session ID:
SC1004
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Speakers:
John Stone
- University of Illinois at Urbana-Champaign
Abstract:
This talk will present recent successes in the use of GPUs to accelerate interactive visualization and analysis tasks on desktop computers, and batch-mode simulation and analysis jobs on GPU-accelerated HPC clusters. We''ll present Fermi-specific algorithms and optimizations and compare with those for other devices. We''ll also present performance and performance/watt results for NAMD molecular dynamics simulations and VMD analysis calculations on GPU clusters, and conclude with a discussion of ongoing work and future opportunities for GPU acceleration, particularly as applied to the analysis of petascale simulations of large biomolecular complexes and long simulation timescales.
This talk will present recent successes in the use of GPUs to accelerate interactive visualization and analysis tasks on desktop computers, and batch-mode simulation and analysis jobs on GPU-accelerated HPC clusters. We''ll present Fermi-specific algorithms and optimizations and compare with those for other devices. We''ll also present performance and performance/watt results for NAMD molecular dynamics simulations and VMD analysis calculations on GPU clusters, and conclude with a discussion of ongoing work and future opportunities for GPU acceleration, particularly as applied to the analysis of petascale simulations of large biomolecular complexes and long simulation timescales.   Back
 
Topics:
Molecular Dynamics, Developer - Algorithms, HPC and AI, Life & Material Science
Type:
Talk
Event:
GTC Silicon Valley
Year:
2010
Session ID:
S102073
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Speakers:
John Stone
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana Champaign
 
Topics:
Molecular Dynamics, Life & Material Science
Type:
Talk
Event:
Supercomputing
Year:
2009
Session ID:
SC0904
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Speakers:
John Stone
Abstract:
State-of-the-art graphics processing units (GPUs) contain hundreds of processing units and are able to perform trillions of floating point arithmetic operations per second. The newly available computational power brought by GPUs is enabling a new generation of scientific and engineering applications to perform calculations on "personal supercomputers" that previously required HPC clusters or that were otherwise impractical in everyday use. This talk will present recent successes in multi-GPU acceleration in VMD, a molecular dynamics visualization and analysis application in which GPU computing techniques have provided speedups ranging from 10 to over 100 times faster than commodity CPU cores. The talk will describe key challenges and algorithmic strategies involved in achieving high computational performance on GPUs, discuss methods for effectively using multiple GPUs in low-latency calculations that drive interactive visualizations, and will also include some examples of how these performance increases ultimately enable better science.
State-of-the-art graphics processing units (GPUs) contain hundreds of processing units and are able to perform trillions of floating point arithmetic operations per second. The newly available computational power brought by GPUs is enabling a new generation of scientific and engineering applications to perform calculations on "personal supercomputers" that previously required HPC clusters or that were otherwise impractical in everyday use. This talk will present recent successes in multi-GPU acceleration in VMD, a molecular dynamics visualization and analysis application in which GPU computing techniques have provided speedups ranging from 10 to over 100 times faster than commodity CPU cores. The talk will describe key challenges and algorithmic strategies involved in achieving high computational performance on GPUs, discuss methods for effectively using multiple GPUs in low-latency calculations that drive interactive visualizations, and will also include some examples of how these performance increases ultimately enable better science.   Back
 
Topics:
General Interest, Professional Visualisation, Life & Material Science, Molecular Dynamics
Type:
Talk
Event:
GTC Silicon Valley
Year:
2009
Session ID:
S09053
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